7BAL | pdb_00007bal

Crystal structure of SARS-CoV-2 main protease treated with ebselen derivative of MR6-31-2

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6Y2E

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		292	200mM ammonium chloride, 5%glycerol and 20% polyethylene glycol mw. 3350

Crystal Properties
Matthews coefficient	Solvent content
1.98	37.76

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 114.004	α = 90
b = 53.622	β = 100.892
c = 44.545	γ = 90

Symmetry
Space Group	C 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS EIGER2 XE 16M	mirrors	2020-08-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9795	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.85	33.867	99.9	0.075	0.102	0.069	0.997	8.6	3.3		22635

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.85	1.89	99.9		1.079	1.456	0.971	0.446	1.6	3.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6y2e	1.85	33.867	22624	1159	99.81	0.225	0.2239	0.22	0.249	0.25	36.114

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
2.401		0.48	-0.621		-1.829

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.358
r_dihedral_angle_4_deg	15.983
r_dihedral_angle_3_deg	15.115
r_dihedral_angle_1_deg	7.769
r_lrange_it	7.584
r_scangle_it	5.721
r_mcangle_it	4.314
r_scbond_it	4.084
r_mcbond_it	3.288
r_angle_refined_deg	1.572

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.358
r_dihedral_angle_4_deg	15.983
r_dihedral_angle_3_deg	15.115
r_dihedral_angle_1_deg	7.769
r_lrange_it	7.584
r_scangle_it	5.721
r_mcangle_it	4.314
r_scbond_it	4.084
r_mcbond_it	3.288
r_angle_refined_deg	1.572
r_symmetry_nbd_refined	0.426
r_nbtor_refined	0.321
r_symmetry_xyhbond_nbd_refined	0.249
r_nbd_refined	0.219
r_xyhbond_nbd_refined	0.17
r_chiral_restr	0.103
r_gen_planes_refined	0.008
r_bond_refined_d	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2307
Nucleic Acid Atoms
Solvent Atoms	139
Heterogen Atoms	1

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
Aimless	data scaling
MOLREP	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.